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  • corr in DNA (1996)
    and the ergodicity of protein sequences First Pacific Symposium on Biocomputing eds RB Altman AK Dunker L Hunter TE Klein pages 216 219 J Filipski E Svetlova N Avril Fournout P Deschavanne M Bellis 1996 New approaches to the mapping of chromosomal domains Acta Biochim Pol 43 2 289 292 Jan Freund Werner Ebeling and Katja Rateitschak 1996 Self similar sequences and universal scaling of dynamical entropies Physical Review E 54 5 5561 5566 sequence R Himmelreich H Hilbert H Plagens E Pirkl BC Li R Herrmann 1996 Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae Nucleic Acids Research 24 4420 4449 sequence H Inoko N Mizuki T Shiina A Ando M Kimura YY Kikuchi H Kawata K Sugaya T Fukagawa K Matsumoto T Nagata M Taketo K Okumura M Kasahara T Ikemura 1996 Cloning sequencing and evolutionary analyses of the human major histocompatibility complex MHC region DNA Sequence 7 1 31 32 period 10 11 Ilya Ioshikhes Alex Bolshoy Konstantin Derenshteyn Mark Borodovsky Edward N Trifonov 1996 Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences Journal of Molecular Biology 262 2 129 139 abstract repeats J Jurka VV Kapitonov P Klonowski J Walichiewicz AF Smit 1996 Identification of new medium reiteration frequency repeats in the genomes of Primates Rodentia and Lagomorpha Genetica 98 3 235 247 repeats J Jurka P Klonowski V Dagman P Pelton 1996 CENSOR a program for identification and elimination of repetitive elements from DNA sequences Computers Chemistry 20 1 119 121 sequence T Kaneko S Sato H Kotani A Tanaka E Asamizu Y Nakamura N Miyajima M Hirosawa M Sugiura S Sasamoto T Kimura T Hosouchi A Matsuno A Muraki N Nakazaki K Naruo S Okumura S Shimpo C Takeuchi T Wada A Watanabe M Yamada M Yasuda S Tabata 1996 Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp strain PCC6803 II Sequence determination of the entire genome and assignment of potential protein coding regions DNA Research 3 109 136 repeats V Kapitonov J Jurka 1996 The age of Alu subfamilies Journal of Molecular Evolution 42 1 59 65 dna music Ross D King Colin G Angus 1996 PM protein music Computer Applications in Biosciences 12 3 251 252 MY Leung GM March TP Speed 1996 Over and under representation of short oligonucleotides in herpes virus genomes Journal of Computational Biology 3 3 345 360 Pietro Liò Antonio Politi Stefano Ruffo Marcello Buiatti 1996 Analysis of genomic patchiness of Haemophilus influenzae and Saccharomyces cerevisiae chromosomes Journal of Theoretical Biology 183 4 455 469 Dec 21 abstract a symmetry JR Lobry 1996 Asymmetric substitution patterns in the two DNA strands of bacteria Molecular Biology and Evolution 13 660 665 abstract Medline entry a symmetry JR Lobry 1996 Origin of replication of Mycoplasma genitalium Science 272 745 746 V Ju Makeev GK Frank VG Tumanyan 1996 Statistics of periodic patterns in the sequences of human introns Biophysics 41 1 263 268 V Ju Makeev VG Tumanyan 1996

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1996.html (2012-11-26)
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  • corr in DNA (1995)
    biopolymers Fractals 3 1 7 22 isochore L Duret D Mouchiroud M Gouy 1995 Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC rich isochores Journal of Molecular Evolution 40 308 317 Werner Ebeling Alexander Neiman Thorsten Pvschel 1995 Dynamic entropies long range correlations and fluctuations in complex linear structures in Coherent Approach to Fluctuations Proc Hayashibara Forum 95 ed M Suzuki World Scientific abstract PDF Martin Farach Michiel Noordewier Serap Savari Larry Shepp Abraham Wyner Jacob Ziv 1995 On the entropy of DNA algorithms and measurements based on memory and rapid convergence Proceedings of the sixth annual ACM SIAM symposium on Discrete algorithms pp 48 57 isochore T Fukagawa K Sugaya K Matsumoto K Okumura A Ando H Inoko T Ikemura 1995 A boundary of long range G C mosaic domains in the human MHC locus pseudoautosomal boundary like sequence exists near the boundary Genomics 25 1 184 191 sequence RD Fleischmann MD Adams O White RA Clayton EF Kirkness AR Kerlavage CJ Bult JF Tomb BA Dougherty JM Merrick K McKenney G Sutton W FitzHugh C Fields JD Gocayne J Scott R Shirley LI Liu A Glodek JM Kelley JF Weidman CA Phillips T Spriggs E Hedblom MD Cotton TR Utterback MC Hanna DT Nguyen DM Saudek RC Brandon LD Fine JL Fritchman JL Fuhrmann NSM Geoghagen CL Gnehm LA McDonald KV Small CM Fraser HQ Smith JC Venter 1995 Whole genome random sequencing and assembly of Haemophilus influenzae Rd Science 269 496 512 a symmetry DR Forsdyke 1995 Relative roles of primary sequence and G C in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species Journal of Molecular Evolution 41 5 573 581 Medline entry sequence CM Fraser JD Gocayne O White MD Adams RA Clayton RD Fleischmann CJ Bult AR Kerlavage G Sutton JM Kelley JL Fritchman JF Weidman KV Small M Sandusky J Fuhrmann D Nguyen TR Utterback DM Saudek CA Phillips JM Merrick JF Tomb BA Dougherty KF Bott PC Hu TS Lucier SN Peterson HO Smith CA Hutchison III JC Venter 1995 The minimal gene complement of Mycoplasma genitalium Science 270 397 403 MS Gelfand 1995 FANS REF a bibliography on statistics and functional analysis of nucleotide sequences Computer Applications in Biosciences 11 5 541 S Hannenhalli P Pevzner 1995 Transforming men into mice polynomial algorithm for genomic distance problems Proceedings of IEEE Symposium of the Foundations of Computer Science pp 581 592 Hanspeter Herzel Ivo Große 1995 Measuring correlations in symbolic sequences Physica A 216 518 542 abstract H Herzel W Ebeling AO Schmitt MA Jimenez Montano 1995 Entropies and lexicographic analysis of biosequences in From Simplicity to Complexity in Chemistry and Beyond eds A Muller A Dress F Vogtle Vierweg Verlag Braunschweig abstract repeats J Jurka C Pethiyagoda 1995 Simple repetitive DNA sequences from primates compilation and analysis Journal of Molecular Evolution 40 2 120 126 protein S Karlin 1995 Statistical significance of sequence patterns in proteins Current Opinion in Structural

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1995.html (2012-11-26)
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  • corr in DNA (1994)
    mutual correlations ordering and long range modulations in genomic nucleotide sequences for viruses Journal of Biomolecular Structure and Dynamics 12 2 271 299 abstract VR Chechetkin AY Turygin 1994 On the spectral criteria of disorder in nonperiodic sequences application to inflation models symbolic dynamics and DNA sequences Journal of Physics A 27 14 4875 4898 abstract protein I Cosic 1994 Macromolecular boiactivityL is it resonant interaction between macromolecules theory and applications IEEE Transactions on Biomedical Engineer 41 12 1101 1114 G Gutierrez JL Oliver A Marin 1994 On the origin of the periodicity of three in protein coding DNA sequences Journal of Theoretical Biology 167 4 413 414 protein J Heringa 1994 The evolution and recognition of protein sequence repeats Computers Chemistry 18 3 233 243 H Herzel W Ebeling AO Schmitt 1994 Entropies of biosequences the role of repeats Physical Review E 50 6 5061 5071 abstract PDF H Herzel A Schmitt W Ebeling 1994 Finite sample effects in sequence analysis Chaos Solitons Fractals 4 97 113 VV Kapitonov II Titov 1994 Introns order and long range correlations in nucleotide sequences in Russian Doklady Akademii Nauk 337 6 810 812 S Karlin 1994 Statistical studies of biomolecular sequences score based methods Philosophical Transactions of the Royal Society B Biological Sciences 344 1310 391 402 Medline entry S Karlin I Ladunga 1994 Comparisons of eukaryotic genomic sequences Proceedings of the National Academy of Sciences 91 26 12832 12836 Medline entry S Karlin I Ladunga BE Blaisdell 1994 Heterogeneity of genomes measures and values Proceedings of the National Academy of Sciences 91 26 12837 12841 Medline entry MY Leung G Schachtel HS Yu 1994 Scan statistics and DNA sequence analysis the search for an origin of replication in a virus Nolnear World 1 445 471 W Li TG Marr K Kaneko 1994 Understanding long range correlations in DNA sequences Physica D 75 1 3 392 416 erratum 82 217 1995 abstract abstract P Li oacute S Ruffo M Buiatti 1994 Third codon G C periodicity as a possible signal for an internal selective constraint Journal of Theoretical Biology 171 2 215 223 Nov 21 abstract a symmetry Jan Mrazek Jaroslav Kypr 1994 Biased distribution of Adenine and Thymine in gene nucleotide sequences Journal of Molecular Evolution 39 439 447 A Nandy 1994 A new graphical representation and analysis of DNA sequence structure I methodology and application to globin genes Current Science 66 4 309 314 A Nandy 1994 Graphical representation of long DNA sequences Current Science 66 11 821 SM Ossadnik SV Buldyrev AL Goldberger S Havlin RN Mantegna CK Peng M Simon HE Stanley 1994 Correlation approach to identify coding regions in DNA sequences Biophysical Journal 67 1 64 70 abstract protein VS Pande AY Grosberg T Tanaka 1994 Nonrandomness in protein sequences evidence for a physically driven stage of evolution Proceedings of the National Academy of Sciences 91 26 12972 12975 abstract CK Peng SV Buldyrev S Havlin M Simon HE Stanley AL Goldberger 1994 Mosaic organization of DNA

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1994.html (2012-11-26)
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  • corr in DNA (1993)
    needed in Russian Biofizika 38 1 75 83 abstract repeats J Jurka 1993 A new subfamily of recently retroposed human Alu repeats Nucleic Acids Research 21 9 2252 repeats J Jurka DJ Kaplan CH Duncan J Walichiewicz A Milosavljevic G Murali JF Solus 1993 Identification and characterization of new human medium reiteration frequency repeats Nucleic Acids Research 21 5 1273 1279 S Karlin BE Blaisdell R Sapolsky L Cardon C Burge 1993 Assessments of DNA inhomogeneities in yeast chromosome III Nucleic Acids Research 21 703 711 Medline entry S Karlin V Brendel 1993 Patchiness and correlations in DNA sequences Science 259 677 680 abstract Medline entry Graham J King 1993 Stability structure and complexity of yeast chromosome III Nucleic Acids Research 21 18 4239 4245 abstract D Larhammar CA Chatzidimitriou Dreismann 1993 Biological origins of long range correlations and compositional variations in DNA Nucleic Acids Research 21 22 5167 5170 abstract repeats A Milosavljevic J Jurka 1993 Discovering simple DNA sequences by the algorithmic significance method Computer Applications in Biosciences 9 4 407 411 bending WK Olson NL Marky RL Jernigan VN Zhurkin 1993 Influence of fluctuations on DNA curvature A comparison of flexible and static wedge models of intrinsically bent DNA Journal of Molecular Biology 232 2 530 554 abstract CK Peng SV Buldyrev AL Goldberger S Havlin M Simon HE Stanley 1993 Finite size effects on long range correlations implications for analyzing DNA sequences Physical Review E 47 5 3730 3733 abstract a symmetry VV Prabhu 1993 Symmetry observations in long nucleotide sequences Nucleic Acids Research 21 2797 2800 MD Purugganan 1993 Scale invariant spatial patterns in genome organization Physics Letters A 175 3 4 252 256 abstract abstract isochore G Sabeur G Macaya F Kadi G Bernardi 1993 The isochore patterns of mammalian genomes and their phylogenetic

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1993.html (2012-11-26)
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  • corr in DNA (1992)
    structure of genomes Genomics 13 1056 1064 abstract MS Gelfand CG Kozhukhin PA Pevzner 1992 Extendable words in nucleotide sequences Computer Applications in Biosciences 8 2 129 135 Medline entry repeats J Jurka J Walichiewicz A Milosavljevic 1992 Prototypic sequences for human repetitive DNA Journal of Molecular Evolution 35 4 286 291 S Karlin V Brendel 1992 Chance and statistical significance in protein and DNA sequence analysis Science 257 5066 39 49 Medline entry AK Konopka 1992 Plausible classification codes and local compositional complexity of nucleotide sequences in Lim et al 1992 69 86 W Li 1992 Generating nontrivial long range correlations and 1 f spectra by replication and mutation International Journal of Bifurcation and Chaos 2 1 137 154 abstract W Li K Kaneko 1992 Long range correlation and partial 1 f a spectrum in a noncoding DNA sequence Europhysics Letters 17 7 655 660 abstract W Li K Kaneko 1992 DNA correlations Scientific Correspondence Nature 360 635 636 GS Mani 1992 Long range doublet correlations in DNA and the coding region Journal of Theoretical Biology 158 447 464 PJ Munson RC Taylor GS Michaels 1992 Scientific Correspondence Nature 360 636 S Nee 1992 Scientific Correspondence Nature 357 450 RC Paton 1992 Towards a metaphorical biology Biology and Philosophy 7 3 279 294 abstract CK Peng SV Buldyrev AL Goldberger S Havlin F Sciortino M Simon HE Stanley 1992 Long range correlations in nucleotide sequences Nature 356 168 170 abstract PDF G Pesole N Prunella S Liuni M Attimonelli C Saccone 1992 WORDUP an efficient algorithm for discovering statistically significant patterns in DNA sequences Nucleic Acids Research 20 2871 2875 PA Pevzner 1992 Nucleotide sequences versus Markov models Computers Chemistry 16 103 106 E Pizzi M Attimonelli S Liuni C Frontali and C Saccone 1992 A simple method for

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1992.html (2012-11-26)
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  • corr in DNA (1991)
    Aissani G Bernardi 1991 Compositional properties of telomeric regions from human chromosomes FEBS Letters 295 1 3 22 26 isochore G D Onofrio D Mouchiroud B Aissani C Gautier G Bernardi 1991 Correlations between the compositional properties of human genes codon usage and amino acid composition of proteins Journal of Molecular Biology 32 6 504 510 repeats J Jurka A Milosavljevic 1991 Reconstruction and analysis of human Alu genes Journal of Molecular Evolution 32 2 105 121 repeats DJ Kaplan J Jurka JF Solus CH Duncan 1991 Medium reiteration frequency repetitive sequences in the human genome Nucleic Acids Research 19 17 4731 4738 W Li 1991 Expansion modification systems a model for spatial 1 f spectra Physical Review A 43 10 5240 5260 LF Luo H Li 1991 The statistical correlation of nucleotides in protein coding DNA sequences Bulletin of Mathematical Biology 53 3 345 353 D Mouchiroud G D Onofrio B Aissani G Macaya C Gautier G Bernardi 1991 The distribution of genes in the human genome Gene 100 181 187 R Nussinov 1991 Compositional variations in DNA sequences Computer Applications in Biosciences 7 3 287 293 R Nussinov 1991 The ordering of nucleotides in the DNA strong pyrimidine purine patterns near homooligomer tracts Journal of Theoretical Biology 149 1 21 42 R Nussinov 1991 Long range and symmetry considerations in the DNA DNA Seq 2 2 69 79 R Nussinov 1991 Distinct patterns in the dinucleotide nearest neighbors to G C and A T oligomers in eukaryotic sequences Journal of Molecular Evolution 33 3 259 266 R Nussinov G Smythers 1991 Trends in the 5 vs 3 flanks of oligonucleotides in eukaryotic and prokaryotic genomes the asymmetric roles played by cytosine and guanine Journal of Theoretical Biology 153 1 111 135 period 3 AA Tsonis JB Elsner PA

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1991.html (2012-11-26)
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  • corr in DNA (1990)
    to the origin of chromosomal compartments Advances in Mutagenesis Research vol 2 pp 1 54 Springer Verlag J Filipski J Leblanc T Youdale M Sikorska PR Walker 1990 Periodicity of DNA folding in higher order chromatin structures EMBO Journal 9 1319 1327 YX Fu RN Curnow 1990 Maximum likelihood estimation of multiple change points Biometrika 77 563 573 isochore K Gardiner B Aissani G Bernardi 1990 A compositional map of human chromosome 21 EMBO Journal 9 6 1853 1858 T Ikemura KN Wada S Aota 1990 Giant G C mosaic structures of the human genome found by arrangement of genbank human DNA sequences according to genetic positions Genomics 8 207 216 repeats J Jurka 1990 Novel families of interspersed repetitive elements from the human genome Nucleic Acids Research 18 1 137 141 AK Konopka J Owens 1990 Non contiguous patterns and compositional complexity of nucleic acid sequences in Computers and DNA eds G Bell and T Marr Addison Wesley Redwood City CA pages 147 155 isochore LM Montero J Salinas G Matassi G Bernardi 1990 Gene distribution and isochore organization in the nuclear genome of plants Nucleic Acids Research 18 7 1859 1867 R Nussinov 1990 General nearest neighbor preferences

    Original URL path: http://linkage.rockefeller.edu/dnacorr/1990.html (2012-11-26)
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  • corr in DNA (80s)
    the genome of vertebrates Journal of Molecular Evolution 26 3 198 204 A Muto S Osawa 1987 The guanine and cytosine content of genomic DNA and bacterial evolution Proceedings of the National Academy of Sciences 84 166 169 PDF dna music S Ohno 1987 Repetition as the essence of life on this earth music and genes Hamatol Bluttransfus 31 511 518 abstract T Ohta 1987 A model of evolution for accumulating genetic information Journal of Theoretical Biology 124 199 211 T Ohta 1987 Simulating evolution by gene duplication Genetics 115 207 213 a symmetry CI Wu N Maeda 1987 Inequality in mutation rates of the two strands of DNA Nature 327 169 170 1986 S Aota T Ikemura 1986 Diversity in G C content at the third position of codons in vertebrate genes and its cause Nucleic Acids Research 14 6345 6355 isochore G Bernardi G Bernardi 1986 Compositional constraints and genome evolution Journal of Molecular Evolution 24 1 2 1 11 binding energy KJ Breslauer R Frank H Blocker LA Marky 1986 Predicting DNA duplex stability from the base sequence Proceedings of the National Academy of Sciences 83 11 3746 3750 M de Zamaroczy G Bernardi 1986 The GC clusters of the mitochondrial genome of yeast and their evolutionary origin Gene 41 1 1 22 dna music S Ohno M Ohno The all persuasive principle of repititious recurrences governs not only coding sequence construction but also human endeavour in musical composition Immunogenetics 24 71 78 1986 abstract J Salinas M Zerial J Filipski G Bernardi 1986 Gene distribution and nucleotide sequence organization in the mouse genome European Journal of Biochemistry 160 3 469 478 BD Silverman R Linsker 1986 A measure of DNA periodicity Journal of Theoretical Biology 118 295 300 binding A Wada A Suyama 1986 Local stability of DNA and RNA secondary structure and its relation to biological functions Progress in Biophysics and Molecular Biology 47 113 157 M Zerial J Salinas J Filipski G Bernardi 1986 Gene distribution and nucleotide sequence organization in the human genome European Journal of Biochemistry 160 3 479 485 1985 G Bernardi G Bernardi 1985 Codon usage and genome composition Journal of Molecular Evolution 22 4 363 365 isochore G Bernardi B Olofsson J Filipski M Zerial J Salinas G Cuny M Meunier Rotival F Rodier 1985 The mosaic genome of warm blooded vertebrates Science 228 4702 953 958 M de Zamaroczy G Bernardi 1985 Sequence organization of the mitochondrial genome of yeast a review Gene 37 1 3 1 17 J Jurka MA Savageau 1985 Gene density over the chromosome of Escherichia coli frequency distribution spatial clustering and symmetry Journal of Bacteriology 163 2 806 811 A Wada A Suyama 1985 Third letters in codons counterbanace the G C content of their first and second letters FEBS Letters 188 291 294 bending VB Zhurkin 1985 Sequence dependent bending of DNA and phasing of nucleosomes Journal of Biomolecular Structure Dynamics 2 4 785 804 1984 MJ Bibb PR Findlay MW Johnson

    Original URL path: http://linkage.rockefeller.edu/dnacorr/80s.html (2012-11-26)
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